[2024-01-24 11:43:25,076] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:25,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:25,081] [INFO] DQC Reference Directory: /var/lib/cwl/stge6999dca-6942-4a45-94fd-d88c2ef9ce61/dqc_reference
[2024-01-24 11:43:30,056] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:30,057] [INFO] Task started: Prodigal
[2024-01-24 11:43:30,058] [INFO] Running command: gunzip -c /var/lib/cwl/stge8d42d07-bf61-4b07-8a55-8fe0f53cc049/GCF_017876095.1_ASM1787609v1_genomic.fna.gz | prodigal -d GCF_017876095.1_ASM1787609v1_genomic.fna/cds.fna -a GCF_017876095.1_ASM1787609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:51,469] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:51,470] [INFO] Task started: HMMsearch
[2024-01-24 11:43:51,470] [INFO] Running command: hmmsearch --tblout GCF_017876095.1_ASM1787609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6999dca-6942-4a45-94fd-d88c2ef9ce61/dqc_reference/reference_markers.hmm GCF_017876095.1_ASM1787609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:51,842] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:51,844] [INFO] Found 6/6 markers.
[2024-01-24 11:43:51,915] [INFO] Query marker FASTA was written to GCF_017876095.1_ASM1787609v1_genomic.fna/markers.fasta
[2024-01-24 11:43:51,915] [INFO] Task started: Blastn
[2024-01-24 11:43:51,915] [INFO] Running command: blastn -query GCF_017876095.1_ASM1787609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6999dca-6942-4a45-94fd-d88c2ef9ce61/dqc_reference/reference_markers.fasta -out GCF_017876095.1_ASM1787609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:53,067] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:53,071] [INFO] Selected 17 target genomes.
[2024-01-24 11:43:53,072] [INFO] Target genome list was writen to GCF_017876095.1_ASM1787609v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:53,079] [INFO] Task started: fastANI
[2024-01-24 11:43:53,080] [INFO] Running command: fastANI --query /var/lib/cwl/stge8d42d07-bf61-4b07-8a55-8fe0f53cc049/GCF_017876095.1_ASM1787609v1_genomic.fna.gz --refList GCF_017876095.1_ASM1787609v1_genomic.fna/target_genomes.txt --output GCF_017876095.1_ASM1787609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:25,376] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:25,377] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6999dca-6942-4a45-94fd-d88c2ef9ce61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:25,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6999dca-6942-4a45-94fd-d88c2ef9ce61/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:25,393] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:25,393] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:25,393] [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
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	100.0	2492	2493	95	conclusive
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	89.0872	1724	2493	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	85.4592	1630	2493	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	85.4043	1579	2493	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	85.3377	1577	2493	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	85.2774	1431	2493	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	85.2302	1572	2493	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	85.1902	1611	2493	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	84.9662	1486	2493	95	below_threshold
Azospirillum lipoferum	strain=59b	GCA_008364955.1	193	193	type	True	84.9513	1557	2493	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	84.5699	1450	2493	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	84.057	1291	2493	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	83.4384	1199	2493	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	83.2976	1399	2493	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	83.2341	1261	2493	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	78.0468	717	2493	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.769	461	2493	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:25,395] [INFO] DFAST Taxonomy check result was written to GCF_017876095.1_ASM1787609v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:25,395] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:25,395] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:25,396] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6999dca-6942-4a45-94fd-d88c2ef9ce61/dqc_reference/checkm_data
[2024-01-24 11:44:25,397] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:25,467] [INFO] Task started: CheckM
[2024-01-24 11:44:25,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876095.1_ASM1787609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876095.1_ASM1787609v1_genomic.fna/checkm_input GCF_017876095.1_ASM1787609v1_genomic.fna/checkm_result
[2024-01-24 11:45:42,575] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:42,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:42,606] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:42,607] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:42,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876095.1_ASM1787609v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:42,609] [INFO] Task started: Blastn
[2024-01-24 11:45:42,609] [INFO] Running command: blastn -query GCF_017876095.1_ASM1787609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6999dca-6942-4a45-94fd-d88c2ef9ce61/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876095.1_ASM1787609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:44,806] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:44,811] [INFO] Selected 16 target genomes.
[2024-01-24 11:45:44,812] [INFO] Target genome list was writen to GCF_017876095.1_ASM1787609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:44,824] [INFO] Task started: fastANI
[2024-01-24 11:45:44,825] [INFO] Running command: fastANI --query /var/lib/cwl/stge8d42d07-bf61-4b07-8a55-8fe0f53cc049/GCF_017876095.1_ASM1787609v1_genomic.fna.gz --refList GCF_017876095.1_ASM1787609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876095.1_ASM1787609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:16,737] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:16,759] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:16,760] [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_017876095.1	s__Azospirillum agricola	100.0	2492	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	96.88	96.88	0.87	0.87	2	conclusive
GCF_003989665.1	s__Azospirillum doebereinerae	89.0947	1722	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116095.1	s__Azospirillum sp003116095	85.9469	1538	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	85.45	1572	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003233655.1	s__Azospirillum ramasamyi	85.2577	1433	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923315.1	s__Azospirillum sp003116065	85.2405	1529	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.27	96.11	0.89	0.85	4	-
GCF_013340935.1	s__Azospirillum melinis	85.1793	1583	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.17	95.47	0.91	0.85	4	-
GCF_003116035.1	s__Azospirillum sp003116035	85.1629	1581	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000283655.1	s__Azospirillum lipoferum_C	85.0946	1506	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	85.0805	1606	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008364795.1	s__Azospirillum oryzae	85.0623	1423	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	98.65	97.30	0.92	0.84	3	-
GCF_008364955.1	s__Azospirillum lipoferum	85.0046	1548	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010725.1	s__Azospirillum lipoferum_B	84.8808	1500	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004923295.1	s__Azospirillum sp003115975	84.838	1478	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_017876115.1	s__Azospirillum picis	84.5741	1450	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966125.1	s__Azospirillum griseum	83.3892	1205	2493	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:16,761] [INFO] GTDB search result was written to GCF_017876095.1_ASM1787609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:16,762] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:16,766] [INFO] DFAST_QC result json was written to GCF_017876095.1_ASM1787609v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:16,766] [INFO] DFAST_QC completed!
[2024-01-24 11:46:16,766] [INFO] Total running time: 0h2m52s