[2024-01-24 13:58:10,315] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,317] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,317] [INFO] DQC Reference Directory: /var/lib/cwl/stg629bb3c5-6f31-473d-9343-0db962c6ecc1/dqc_reference
[2024-01-24 13:58:11,585] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,586] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,586] [INFO] Running command: gunzip -c /var/lib/cwl/stge9a5bc10-0cd8-4810-8f13-f43933358640/GCF_008831265.1_ASM883126v1_genomic.fna.gz | prodigal -d GCF_008831265.1_ASM883126v1_genomic.fna/cds.fna -a GCF_008831265.1_ASM883126v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:27,021] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:27,022] [INFO] Task started: HMMsearch
[2024-01-24 13:58:27,022] [INFO] Running command: hmmsearch --tblout GCF_008831265.1_ASM883126v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg629bb3c5-6f31-473d-9343-0db962c6ecc1/dqc_reference/reference_markers.hmm GCF_008831265.1_ASM883126v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:27,349] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:27,351] [INFO] Found 6/6 markers.
[2024-01-24 13:58:27,398] [INFO] Query marker FASTA was written to GCF_008831265.1_ASM883126v1_genomic.fna/markers.fasta
[2024-01-24 13:58:27,399] [INFO] Task started: Blastn
[2024-01-24 13:58:27,399] [INFO] Running command: blastn -query GCF_008831265.1_ASM883126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg629bb3c5-6f31-473d-9343-0db962c6ecc1/dqc_reference/reference_markers.fasta -out GCF_008831265.1_ASM883126v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:28,376] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:28,380] [INFO] Selected 26 target genomes.
[2024-01-24 13:58:28,381] [INFO] Target genome list was writen to GCF_008831265.1_ASM883126v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:28,398] [INFO] Task started: fastANI
[2024-01-24 13:58:28,399] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a5bc10-0cd8-4810-8f13-f43933358640/GCF_008831265.1_ASM883126v1_genomic.fna.gz --refList GCF_008831265.1_ASM883126v1_genomic.fna/target_genomes.txt --output GCF_008831265.1_ASM883126v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:52,262] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:52,263] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg629bb3c5-6f31-473d-9343-0db962c6ecc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:52,263] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg629bb3c5-6f31-473d-9343-0db962c6ecc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:52,289] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:52,290] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:52,290] [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
Noviherbaspirillum aridicola	strain=NCCP-691	GCA_019656455.1	2849687	2849687	type	True	79.5991	456	1489	95	below_threshold
Noviherbaspirillum humi	strain=U15	GCA_900188095.1	1688639	1688639	type	True	79.2357	485	1489	95	below_threshold
Oxalicibacterium flavum	strain=CCM 7086	GCA_014635065.1	179467	179467	type	True	79.2118	366	1489	95	below_threshold
Noviherbaspirillum malthae	strain=CC-AFH3	GCA_015352985.1	1260987	1260987	type	True	79.0258	464	1489	95	below_threshold
Noviherbaspirillum pedocola	strain=DKR-6	GCA_016632335.1	2801341	2801341	type	True	79.0233	469	1489	95	below_threshold
Herbaspirillum camelliae	strain=WT00C	GCA_001929405.1	1892903	1892903	type	True	79.0089	370	1489	95	below_threshold
Herbaspirillum robiniae	strain=HZ10	GCA_002213415.1	2014887	2014887	type	True	78.9755	456	1489	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_001040945.1	964	964	type	True	78.9199	387	1489	95	below_threshold
Noviherbaspirillum denitrificans	strain=TSA40	GCA_002211445.1	1968433	1968433	type	True	78.8182	425	1489	95	below_threshold
Herbaspirillum chlorophenolicum	strain=NBRC 102525	GCA_001571165.1	211589	211589	type	True	78.8089	378	1489	95	below_threshold
Herbaspirillum seropedicae	strain=Z67	GCA_013180375.1	964	964	type	True	78.8075	378	1489	95	below_threshold
Collimonas fungivorans	strain=Ter6	GCA_001584145.1	158899	158899	type	True	78.611	381	1489	95	below_threshold
Collimonas pratensis	strain=Ter91	GCA_001584185.1	279113	279113	type	True	78.5704	365	1489	95	below_threshold
Herbaspirillum aquaticum	strain=IEH 4430	GCA_002213425.1	568783	568783	type	True	78.5676	384	1489	95	below_threshold
Herbaspirillum lusitanum	strain=P6-12	GCA_000256565.1	213312	213312	type	True	78.5578	348	1489	95	below_threshold
Massilia atriviolacea	strain=SOD	GCA_003953935.1	2495579	2495579	type	True	78.5434	411	1489	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	78.5153	432	1489	95	below_threshold
Noviherbaspirillum autotrophicum	strain=TSA66	GCA_000818395.1	709839	709839	type	True	78.4923	396	1489	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	78.4918	410	1489	95	below_threshold
Massilia arenosa	strain=MC02	GCA_004614185.1	2561931	2561931	type	True	78.4076	334	1489	95	below_threshold
Massilia eurypsychrophila	strain=JCM 30074	GCA_002760655.1	1485217	1485217	type	True	78.3692	427	1489	95	below_threshold
Noviherbaspirillum massiliense	strain=JC206	GCA_000312045.1	1465823	1465823	type	True	78.3665	383	1489	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	78.3323	417	1489	95	below_threshold
Massilia psychrophila	strain=JCM 30813	GCA_002760665.1	1603353	1603353	type	True	78.2808	357	1489	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	78.2383	370	1489	95	below_threshold
Massilia psychrophila	strain=CGMCC 1.15196	GCA_014641415.1	1603353	1603353	type	True	78.2173	361	1489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:52,292] [INFO] DFAST Taxonomy check result was written to GCF_008831265.1_ASM883126v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:52,293] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:52,293] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:52,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg629bb3c5-6f31-473d-9343-0db962c6ecc1/dqc_reference/checkm_data
[2024-01-24 13:58:52,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:52,341] [INFO] Task started: CheckM
[2024-01-24 13:58:52,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008831265.1_ASM883126v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008831265.1_ASM883126v1_genomic.fna/checkm_input GCF_008831265.1_ASM883126v1_genomic.fna/checkm_result
[2024-01-24 13:59:42,212] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:42,214] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:42,234] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:42,234] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:42,235] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008831265.1_ASM883126v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:42,235] [INFO] Task started: Blastn
[2024-01-24 13:59:42,235] [INFO] Running command: blastn -query GCF_008831265.1_ASM883126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg629bb3c5-6f31-473d-9343-0db962c6ecc1/dqc_reference/reference_markers_gtdb.fasta -out GCF_008831265.1_ASM883126v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:44,167] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:44,172] [INFO] Selected 24 target genomes.
[2024-01-24 13:59:44,172] [INFO] Target genome list was writen to GCF_008831265.1_ASM883126v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:44,194] [INFO] Task started: fastANI
[2024-01-24 13:59:44,195] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a5bc10-0cd8-4810-8f13-f43933358640/GCF_008831265.1_ASM883126v1_genomic.fna.gz --refList GCF_008831265.1_ASM883126v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008831265.1_ASM883126v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:04,678] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:04,701] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:04,701] [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_008831265.1	s__Lacisediminimonas profundi	100.0	1483	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lacisediminimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016467405.1	s__Lacisediminimonas sp016467405	79.955	651	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Lacisediminimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015352955.1	s__Noviherbaspirillum_A soli	79.6431	532	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590835.1	s__Paucimonas sp003590835	79.2398	393	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188095.1	s__Noviherbaspirillum humi	79.2261	486	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635065.1	s__Oxalicibacterium flavum	79.1646	364	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007874125.1	s__Noviherbaspirillum sp007874125	79.0336	436	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016632335.1	s__Noviherbaspirillum_A pedocola	79.0201	469	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002213415.1	s__Herbaspirillum robiniae	79.0107	452	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.55	98.54	0.93	0.92	3	-
GCF_000221045.1	s__Collimonas fungivorans_A	78.9382	382	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Collimonas	95.0	95.12	95.12	0.85	0.85	2	-
GCA_004570315.1	s__Noviherbaspirillum sp004570315	78.9356	373	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Noviherbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001040945.1	s__Herbaspirillum seropedicae	78.9083	388	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	98.53	96.09	0.94	0.89	6	-
GCF_004114795.1	s__Paucimonas sp004114795	78.8894	362	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paucimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004134995.1	s__Herbaspirillum sp004134995	78.7745	331	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635845.1	s__Oxalicibacterium solurbis	78.6695	321	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Oxalicibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377845.1	s__CAILRJ01 sp014377845	78.6375	342	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAILRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019232795.1	s__PKWO01 sp019232795	78.5763	247	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__PKWO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000282575.1	s__Herbaspirillum sp000282575	78.5553	347	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Herbaspirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000344615.1	s__Janthinobacterium sp000344615	78.4359	442	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Janthinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760655.1	s__Massilia eurypsychrophila	78.354	428	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857595.1	s__Pseudoduganella aquatica_A	78.3202	416	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002760665.1	s__Massilia psychrophila	78.27	358	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900109645.1	s__Duganella sp900109645	78.0422	364	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Duganella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001770235.1	s__RBG-16-58-11 sp001770235	75.7932	61	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__RBG-16-58-11;g__RBG-16-58-11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:04,703] [INFO] GTDB search result was written to GCF_008831265.1_ASM883126v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:04,703] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:04,708] [INFO] DFAST_QC result json was written to GCF_008831265.1_ASM883126v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:04,709] [INFO] DFAST_QC completed!
[2024-01-24 14:00:04,709] [INFO] Total running time: 0h1m54s