[2024-01-24 12:36:35,050] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:35,053] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:35,054] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4b3a34e-50b0-45b1-b982-340ba1defcfe/dqc_reference
[2024-01-24 12:36:36,261] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:36,261] [INFO] Task started: Prodigal
[2024-01-24 12:36:36,262] [INFO] Running command: gunzip -c /var/lib/cwl/stgda39a266-728a-4698-a760-6484ea1be817/GCF_019684215.1_ASM1968421v1_genomic.fna.gz | prodigal -d GCF_019684215.1_ASM1968421v1_genomic.fna/cds.fna -a GCF_019684215.1_ASM1968421v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:54,699] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:54,700] [INFO] Task started: HMMsearch
[2024-01-24 12:36:54,700] [INFO] Running command: hmmsearch --tblout GCF_019684215.1_ASM1968421v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4b3a34e-50b0-45b1-b982-340ba1defcfe/dqc_reference/reference_markers.hmm GCF_019684215.1_ASM1968421v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:55,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:55,082] [INFO] Found 6/6 markers.
[2024-01-24 12:36:55,136] [INFO] Query marker FASTA was written to GCF_019684215.1_ASM1968421v1_genomic.fna/markers.fasta
[2024-01-24 12:36:55,136] [INFO] Task started: Blastn
[2024-01-24 12:36:55,136] [INFO] Running command: blastn -query GCF_019684215.1_ASM1968421v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4b3a34e-50b0-45b1-b982-340ba1defcfe/dqc_reference/reference_markers.fasta -out GCF_019684215.1_ASM1968421v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:56,120] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:56,124] [INFO] Selected 15 target genomes.
[2024-01-24 12:36:56,124] [INFO] Target genome list was writen to GCF_019684215.1_ASM1968421v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:56,187] [INFO] Task started: fastANI
[2024-01-24 12:36:56,187] [INFO] Running command: fastANI --query /var/lib/cwl/stgda39a266-728a-4698-a760-6484ea1be817/GCF_019684215.1_ASM1968421v1_genomic.fna.gz --refList GCF_019684215.1_ASM1968421v1_genomic.fna/target_genomes.txt --output GCF_019684215.1_ASM1968421v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:18,738] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:18,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4b3a34e-50b0-45b1-b982-340ba1defcfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:18,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4b3a34e-50b0-45b1-b982-340ba1defcfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:18,755] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:37:18,756] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:18,756] [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 bangladeshense	strain=BLR175	GCA_019684215.1	1138189	1138189	type	True	100.0	2110	2113	95	conclusive
Rhizobium bangladeshense	strain=BLR175	GCA_017357245.1	1138189	1138189	type	True	99.9998	2109	2113	95	conclusive
Rhizobium aethiopicum	strain=HBR26	GCA_900094625.1	1138170	1138170	type	True	90.9074	1724	2113	95	below_threshold
Rhizobium esperanzae	strain=CNPSo 668	GCA_002204185.1	1967781	1967781	suspected-type	True	89.8324	1668	2113	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_017352135.1	1138194	1138194	type	True	89.6033	1762	2113	95	below_threshold
Rhizobium lentis	strain=BLR27	GCA_019684715.1	1138194	1138194	type	True	89.5933	1763	2113	95	below_threshold
Rhizobium etli	strain=CFN 42	GCA_000092045.1	29449	29449	suspected-type	True	89.373	1718	2113	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	88.2057	1611	2113	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	87.3662	1642	2113	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	87.3156	1644	2113	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	87.208	1510	2113	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	86.9351	1590	2113	95	below_threshold
Rhizobium mongolense subsp. loessense	strain=CGMCC 1.3401	GCA_900099775.1	158890	57676	type	True	81.2004	1101	2113	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	80.0837	917	2113	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	79.3109	642	2113	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:18,757] [INFO] DFAST Taxonomy check result was written to GCF_019684215.1_ASM1968421v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:18,758] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:18,758] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:18,758] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4b3a34e-50b0-45b1-b982-340ba1defcfe/dqc_reference/checkm_data
[2024-01-24 12:37:18,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:18,821] [INFO] Task started: CheckM
[2024-01-24 12:37:18,821] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019684215.1_ASM1968421v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019684215.1_ASM1968421v1_genomic.fna/checkm_input GCF_019684215.1_ASM1968421v1_genomic.fna/checkm_result
[2024-01-24 12:38:13,108] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:13,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:13,135] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:13,135] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:13,136] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019684215.1_ASM1968421v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:13,136] [INFO] Task started: Blastn
[2024-01-24 12:38:13,136] [INFO] Running command: blastn -query GCF_019684215.1_ASM1968421v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4b3a34e-50b0-45b1-b982-340ba1defcfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_019684215.1_ASM1968421v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:15,092] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:15,097] [INFO] Selected 12 target genomes.
[2024-01-24 12:38:15,098] [INFO] Target genome list was writen to GCF_019684215.1_ASM1968421v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:15,116] [INFO] Task started: fastANI
[2024-01-24 12:38:15,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgda39a266-728a-4698-a760-6484ea1be817/GCF_019684215.1_ASM1968421v1_genomic.fna.gz --refList GCF_019684215.1_ASM1968421v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019684215.1_ASM1968421v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:34,169] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:34,185] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:34,185] [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_017357245.1	s__Rhizobium bangladeshense	99.9998	2110	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.42	98.08	0.93	0.91	5	conclusive
GCF_014197535.1	s__Rhizobium aethiopicum_A	90.4216	1684	2113	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	90.3097	1766	2113	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	89.8705	1717	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	97.28	97.20	0.87	0.86	3	-
GCF_002204185.1	s__Rhizobium esperanzae	89.8252	1668	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.10	96.05	0.88	0.87	12	-
GCF_017352135.1	s__Rhizobium lentis	89.6015	1764	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092045.1	s__Rhizobium etli	89.3668	1719	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.53	98.53	0.90	0.89	3	-
GCF_002531955.1	s__Rhizobium sp002531955	88.2173	1607	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.59	95.76	0.89	0.85	5	-
GCF_002531825.1	s__Rhizobium sp002531825	87.7671	1545	2113	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	87.5298	1572	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	96.97	96.97	0.89	0.89	2	-
GCF_003985145.1	s__Rhizobium anhuiense	87.3656	1642	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.85	98.46	0.91	0.88	19	-
GCF_001187535.1	s__Rhizobium ecuadorense	87.1996	1511	2113	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Rhizobium	95.0	98.51	98.31	0.89	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:34,187] [INFO] GTDB search result was written to GCF_019684215.1_ASM1968421v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:34,188] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:34,191] [INFO] DFAST_QC result json was written to GCF_019684215.1_ASM1968421v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:34,191] [INFO] DFAST_QC completed!
[2024-01-24 12:38:34,192] [INFO] Total running time: 0h1m59s