[2024-01-24 13:02:04,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:02:04,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:02:04,298] [INFO] DQC Reference Directory: /var/lib/cwl/stg49ffbfc2-47d9-4406-97ea-c98a104229dc/dqc_reference
[2024-01-24 13:02:05,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:02:05,640] [INFO] Task started: Prodigal
[2024-01-24 13:02:05,640] [INFO] Running command: gunzip -c /var/lib/cwl/stgea61a380-4b8e-4d75-a052-5a78466c52fe/GCF_000092045.1_ASM9204v1_genomic.fna.gz | prodigal -d GCF_000092045.1_ASM9204v1_genomic.fna/cds.fna -a GCF_000092045.1_ASM9204v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:02:25,298] [INFO] Task succeeded: Prodigal
[2024-01-24 13:02:25,299] [INFO] Task started: HMMsearch
[2024-01-24 13:02:25,299] [INFO] Running command: hmmsearch --tblout GCF_000092045.1_ASM9204v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49ffbfc2-47d9-4406-97ea-c98a104229dc/dqc_reference/reference_markers.hmm GCF_000092045.1_ASM9204v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:02:25,732] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:02:25,734] [INFO] Found 6/6 markers.
[2024-01-24 13:02:25,792] [INFO] Query marker FASTA was written to GCF_000092045.1_ASM9204v1_genomic.fna/markers.fasta
[2024-01-24 13:02:25,792] [INFO] Task started: Blastn
[2024-01-24 13:02:25,793] [INFO] Running command: blastn -query GCF_000092045.1_ASM9204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49ffbfc2-47d9-4406-97ea-c98a104229dc/dqc_reference/reference_markers.fasta -out GCF_000092045.1_ASM9204v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:26,834] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:26,838] [INFO] Selected 16 target genomes.
[2024-01-24 13:02:26,839] [INFO] Target genome list was writen to GCF_000092045.1_ASM9204v1_genomic.fna/target_genomes.txt
[2024-01-24 13:02:26,842] [INFO] Task started: fastANI
[2024-01-24 13:02:26,843] [INFO] Running command: fastANI --query /var/lib/cwl/stgea61a380-4b8e-4d75-a052-5a78466c52fe/GCF_000092045.1_ASM9204v1_genomic.fna.gz --refList GCF_000092045.1_ASM9204v1_genomic.fna/target_genomes.txt --output GCF_000092045.1_ASM9204v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:02:52,223] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:52,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49ffbfc2-47d9-4406-97ea-c98a104229dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:02:52,224] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49ffbfc2-47d9-4406-97ea-c98a104229dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:02:52,240] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:02:52,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:02:52,240] [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 etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	100.0	2170	2173	95	conclusive
Rhizobium esperanzae	strain=CNPSo 668	GCA_002204185.1	1967781	1967781	suspected-type	True	93.3701	1814	2173	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	90.0117	1723	2173	95	below_threshold
Rhizobium phaseoli	strain=ATCC 14482	GCA_003985125.1	396	396	type	True	89.98	1751	2173	95	below_threshold
Rhizobium sophoriradicis	strain=CCBAU 03470	GCA_003939025.1	1535245	1535245	type	True	89.9052	1745	2173	95	below_threshold
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	89.8698	1764	2173	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_017357245.1	1138189	1138189	type	True	89.3911	1708	2173	95	below_threshold
Rhizobium bangladeshense	strain=BLR175	GCA_019684215.1	1138189	1138189	type	True	89.376	1723	2173	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	88.8567	1650	2173	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_019684715.1	1138194	1138194	type	True	88.6992	1656	2173	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	88.5923	1646	2173	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	88.3739	1706	2173	95	below_threshold
Rhizobium sophorae	strain=CCBAU 03386	GCA_013087515.1	1535242	1535242	type	True	87.1856	1620	2173	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.2131	1123	2173	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.3772	930	2173	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	80.2059	726	2173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:02:52,242] [INFO] DFAST Taxonomy check result was written to GCF_000092045.1_ASM9204v1_genomic.fna/tc_result.tsv
[2024-01-24 13:02:52,242] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:02:52,242] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:02:52,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49ffbfc2-47d9-4406-97ea-c98a104229dc/dqc_reference/checkm_data
[2024-01-24 13:02:52,244] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:02:52,306] [INFO] Task started: CheckM
[2024-01-24 13:02:52,306] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000092045.1_ASM9204v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000092045.1_ASM9204v1_genomic.fna/checkm_input GCF_000092045.1_ASM9204v1_genomic.fna/checkm_result
[2024-01-24 13:03:48,501] [INFO] Task succeeded: CheckM
[2024-01-24 13:03:48,503] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:03:48,530] [INFO] ===== Completeness check finished =====
[2024-01-24 13:03:48,531] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:03:48,531] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000092045.1_ASM9204v1_genomic.fna/markers.fasta)
[2024-01-24 13:03:48,532] [INFO] Task started: Blastn
[2024-01-24 13:03:48,532] [INFO] Running command: blastn -query GCF_000092045.1_ASM9204v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49ffbfc2-47d9-4406-97ea-c98a104229dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_000092045.1_ASM9204v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:03:50,558] [INFO] Task succeeded: Blastn
[2024-01-24 13:03:50,562] [INFO] Selected 11 target genomes.
[2024-01-24 13:03:50,562] [INFO] Target genome list was writen to GCF_000092045.1_ASM9204v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:03:50,569] [INFO] Task started: fastANI
[2024-01-24 13:03:50,569] [INFO] Running command: fastANI --query /var/lib/cwl/stgea61a380-4b8e-4d75-a052-5a78466c52fe/GCF_000092045.1_ASM9204v1_genomic.fna.gz --refList GCF_000092045.1_ASM9204v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000092045.1_ASM9204v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:04:08,577] [INFO] Task succeeded: fastANI
[2024-01-24 13:04:08,597] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:04:08,597] [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_000092045.1	s__Rhizobium etli	100.0	2170	2173	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.53	98.53	0.90	0.89	3	conclusive
GCF_002204185.1	s__Rhizobium esperanzae	93.3611	1815	2173	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.10	96.05	0.88	0.87	12	-
GCF_014197535.1	s__Rhizobium aethiopicum_A	92.3422	1805	2173	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	99.98	99.98	0.98	0.98	2	-
GCF_017948245.1	s__Rhizobium sp017948245	91.5168	1746	2173	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117485.1	s__Rhizobium sp002117485	91.093	1784	2173	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.28	97.20	0.87	0.86	3	-
GCF_002531955.1	s__Rhizobium sp002531955	90.1979	1758	2173	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.59	95.76	0.89	0.85	5	-
GCF_003985125.1	s__Rhizobium phaseoli	89.9757	1752	2173	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.51	96.92	0.91	0.87	41	-
GCF_900094625.1	s__Rhizobium aethiopicum	89.8435	1767	2173	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.33	98.33	0.89	0.89	2	-
GCF_017357245.1	s__Rhizobium bangladeshense	89.398	1707	2173	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.42	98.08	0.93	0.91	5	-
GCF_002211285.1	s__Rhizobium sp002211285	88.6203	1556	2173	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211305.1	s__Rhizobium sp002211305	88.2084	1627	2173	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.97	96.97	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:04:08,599] [INFO] GTDB search result was written to GCF_000092045.1_ASM9204v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:04:08,600] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:04:08,605] [INFO] DFAST_QC result json was written to GCF_000092045.1_ASM9204v1_genomic.fna/dqc_result.json
[2024-01-24 13:04:08,605] [INFO] DFAST_QC completed!
[2024-01-24 13:04:08,605] [INFO] Total running time: 0h2m4s