[2024-01-24 13:58:10,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,259] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,260] [INFO] DQC Reference Directory: /var/lib/cwl/stgf929d6ca-4c84-4565-a7bb-a268b1fbd5a0/dqc_reference
[2024-01-24 13:58:11,352] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,352] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,353] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2ed5069-2956-4a76-ba83-6e6999524dab/GCF_019966595.1_ASM1996659v1_genomic.fna.gz | prodigal -d GCF_019966595.1_ASM1996659v1_genomic.fna/cds.fna -a GCF_019966595.1_ASM1996659v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:24,598] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:24,598] [INFO] Task started: HMMsearch
[2024-01-24 13:58:24,599] [INFO] Running command: hmmsearch --tblout GCF_019966595.1_ASM1996659v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf929d6ca-4c84-4565-a7bb-a268b1fbd5a0/dqc_reference/reference_markers.hmm GCF_019966595.1_ASM1996659v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:24,836] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:24,837] [INFO] Found 6/6 markers.
[2024-01-24 13:58:24,878] [INFO] Query marker FASTA was written to GCF_019966595.1_ASM1996659v1_genomic.fna/markers.fasta
[2024-01-24 13:58:24,878] [INFO] Task started: Blastn
[2024-01-24 13:58:24,878] [INFO] Running command: blastn -query GCF_019966595.1_ASM1996659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf929d6ca-4c84-4565-a7bb-a268b1fbd5a0/dqc_reference/reference_markers.fasta -out GCF_019966595.1_ASM1996659v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:25,828] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:25,831] [INFO] Selected 18 target genomes.
[2024-01-24 13:58:25,831] [INFO] Target genome list was writen to GCF_019966595.1_ASM1996659v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:25,869] [INFO] Task started: fastANI
[2024-01-24 13:58:25,869] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2ed5069-2956-4a76-ba83-6e6999524dab/GCF_019966595.1_ASM1996659v1_genomic.fna.gz --refList GCF_019966595.1_ASM1996659v1_genomic.fna/target_genomes.txt --output GCF_019966595.1_ASM1996659v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:42,716] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:42,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf929d6ca-4c84-4565-a7bb-a268b1fbd5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:42,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf929d6ca-4c84-4565-a7bb-a268b1fbd5a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:42,727] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:42,727] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:42,728] [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
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	100.0	1673	1678	95	conclusive
Oricola thermophila	strain=MEBiC13590	GCA_013358405.1	2742145	2742145	type	True	80.3249	703	1678	95	below_threshold
Oricola cellulosilytica	strain=JCM 19534	GCA_019966575.1	1429082	1429082	type	True	78.8508	463	1678	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	78.4069	442	1678	95	below_threshold
Aquibium oceanicum	strain=B7	GCA_001889605.1	1670800	1670800	type	True	78.3922	442	1678	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	78.3478	400	1678	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	78.2615	452	1678	95	below_threshold
Mesorhizobium sediminum	strain=KCTC 42205	GCA_013240295.1	1849104	1849104	type	True	78.1524	397	1678	95	below_threshold
Mesorhizobium onobrychidis	strain=OM4	GCA_024707545.1	2775404	2775404	type	True	78.12	382	1678	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	78.0889	414	1678	95	below_threshold
Aminobacter ciceronei	strain=DSM 15910	GCA_014138625.1	150723	150723	type	True	78.0495	413	1678	95	below_threshold
Nitratireductor alexandrii	strain=Z3-1	GCA_004000215.1	2448161	2448161	type	True	78.029	429	1678	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.9961	387	1678	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	77.995	453	1678	95	below_threshold
Mesorhizobium camelthorni	strain=CCNWXJ 40-4	GCA_011045125.1	475069	475069	type	True	77.9937	392	1678	95	below_threshold
Shinella daejeonensis	strain=JCM 16236	GCA_024281235.1	659017	659017	type	True	77.9485	334	1678	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	77.7517	342	1678	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	77.7333	344	1678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:42,729] [INFO] DFAST Taxonomy check result was written to GCF_019966595.1_ASM1996659v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:42,730] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:42,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:42,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf929d6ca-4c84-4565-a7bb-a268b1fbd5a0/dqc_reference/checkm_data
[2024-01-24 13:58:42,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:42,777] [INFO] Task started: CheckM
[2024-01-24 13:58:42,777] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019966595.1_ASM1996659v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019966595.1_ASM1996659v1_genomic.fna/checkm_input GCF_019966595.1_ASM1996659v1_genomic.fna/checkm_result
[2024-01-24 13:59:22,182] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:22,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:22,203] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:22,203] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:22,204] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019966595.1_ASM1996659v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:22,204] [INFO] Task started: Blastn
[2024-01-24 13:59:22,204] [INFO] Running command: blastn -query GCF_019966595.1_ASM1996659v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf929d6ca-4c84-4565-a7bb-a268b1fbd5a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_019966595.1_ASM1996659v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:24,222] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:24,225] [INFO] Selected 9 target genomes.
[2024-01-24 13:59:24,225] [INFO] Target genome list was writen to GCF_019966595.1_ASM1996659v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:24,231] [INFO] Task started: fastANI
[2024-01-24 13:59:24,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2ed5069-2956-4a76-ba83-6e6999524dab/GCF_019966595.1_ASM1996659v1_genomic.fna.gz --refList GCF_019966595.1_ASM1996659v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019966595.1_ASM1996659v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:33,006] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:33,013] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:59:33,013] [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
GCA_002698425.1	s__Oricola sp002698425	82.7301	966	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706335.1	s__Oricola sp002706335	82.5136	953	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904745.1	s__Oricola sp014904745	81.5429	867	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013358405.1	s__Oricola thermophila	80.3249	703	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331745.1	s__Oricola cellulosilytica	78.8578	473	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Oricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004331955.1	s__Roseitalea porphyridii	78.7445	468	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149475.2	s__Roseitalea stylonematis	78.6115	472	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Roseitalea	95.0	98.99	98.97	0.96	0.95	13	-
GCF_007922615.2	s__Nitratireductor_D sp007922615	78.117	427	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Nitratireductor_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014863355.1	s__Aminobacter carboxidus	78.0706	397	1678	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	98.38	98.38	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:33,014] [INFO] GTDB search result was written to GCF_019966595.1_ASM1996659v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:33,015] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:33,020] [INFO] DFAST_QC result json was written to GCF_019966595.1_ASM1996659v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:33,020] [INFO] DFAST_QC completed!
[2024-01-24 13:59:33,020] [INFO] Total running time: 0h1m23s