[2024-01-25 19:08:05,821] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:08:05,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:08:05,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg7965918c-cc68-4615-97c5-4d92da0c88d8/dqc_reference
[2024-01-25 19:08:07,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:08:07,014] [INFO] Task started: Prodigal
[2024-01-25 19:08:07,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d198d33-42ab-403f-a26e-ca4c2effaa14/GCF_024055665.1_ASM2405566v1_genomic.fna.gz | prodigal -d GCF_024055665.1_ASM2405566v1_genomic.fna/cds.fna -a GCF_024055665.1_ASM2405566v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:08:21,151] [INFO] Task succeeded: Prodigal
[2024-01-25 19:08:21,152] [INFO] Task started: HMMsearch
[2024-01-25 19:08:21,152] [INFO] Running command: hmmsearch --tblout GCF_024055665.1_ASM2405566v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7965918c-cc68-4615-97c5-4d92da0c88d8/dqc_reference/reference_markers.hmm GCF_024055665.1_ASM2405566v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:08:21,479] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:08:21,480] [INFO] Found 6/6 markers.
[2024-01-25 19:08:21,520] [INFO] Query marker FASTA was written to GCF_024055665.1_ASM2405566v1_genomic.fna/markers.fasta
[2024-01-25 19:08:21,521] [INFO] Task started: Blastn
[2024-01-25 19:08:21,521] [INFO] Running command: blastn -query GCF_024055665.1_ASM2405566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7965918c-cc68-4615-97c5-4d92da0c88d8/dqc_reference/reference_markers.fasta -out GCF_024055665.1_ASM2405566v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:08:22,413] [INFO] Task succeeded: Blastn
[2024-01-25 19:08:22,427] [INFO] Selected 11 target genomes.
[2024-01-25 19:08:22,428] [INFO] Target genome list was writen to GCF_024055665.1_ASM2405566v1_genomic.fna/target_genomes.txt
[2024-01-25 19:08:22,440] [INFO] Task started: fastANI
[2024-01-25 19:08:22,440] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d198d33-42ab-403f-a26e-ca4c2effaa14/GCF_024055665.1_ASM2405566v1_genomic.fna.gz --refList GCF_024055665.1_ASM2405566v1_genomic.fna/target_genomes.txt --output GCF_024055665.1_ASM2405566v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:08:34,487] [INFO] Task succeeded: fastANI
[2024-01-25 19:08:34,487] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7965918c-cc68-4615-97c5-4d92da0c88d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:08:34,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7965918c-cc68-4615-97c5-4d92da0c88d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:08:34,496] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:08:34,496] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:08:34,496] [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
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	92.3239	1290	1554	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	92.3205	1212	1554	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	88.2564	1206	1554	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	82.0587	643	1554	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	81.0992	752	1554	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.4493	622	1554	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	79.9382	702	1554	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	79.8798	562	1554	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	79.4981	611	1554	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.0285	598	1554	95	below_threshold
Roseospira goensis	strain=JA135	GCA_014197795.1	391922	391922	type	True	75.5711	205	1554	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:08:34,497] [INFO] DFAST Taxonomy check result was written to GCF_024055665.1_ASM2405566v1_genomic.fna/tc_result.tsv
[2024-01-25 19:08:34,498] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:08:34,498] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:08:34,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7965918c-cc68-4615-97c5-4d92da0c88d8/dqc_reference/checkm_data
[2024-01-25 19:08:34,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:08:34,548] [INFO] Task started: CheckM
[2024-01-25 19:08:34,548] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024055665.1_ASM2405566v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024055665.1_ASM2405566v1_genomic.fna/checkm_input GCF_024055665.1_ASM2405566v1_genomic.fna/checkm_result
[2024-01-25 19:11:09,575] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:09,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:09,594] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:09,595] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:09,596] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024055665.1_ASM2405566v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:09,596] [INFO] Task started: Blastn
[2024-01-25 19:11:09,596] [INFO] Running command: blastn -query GCF_024055665.1_ASM2405566v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7965918c-cc68-4615-97c5-4d92da0c88d8/dqc_reference/reference_markers_gtdb.fasta -out GCF_024055665.1_ASM2405566v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:11,318] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:11,321] [INFO] Selected 17 target genomes.
[2024-01-25 19:11:11,321] [INFO] Target genome list was writen to GCF_024055665.1_ASM2405566v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:11,359] [INFO] Task started: fastANI
[2024-01-25 19:11:11,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d198d33-42ab-403f-a26e-ca4c2effaa14/GCF_024055665.1_ASM2405566v1_genomic.fna.gz --refList GCF_024055665.1_ASM2405566v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024055665.1_ASM2405566v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:28,928] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:28,939] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:11:28,939] [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_000333615.1	s__Ideonella sp000333615	92.3444	1037	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801845.1	s__Ideonella dechloratans	92.3205	1212	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302485.1	s__Ideonella sp017302485	82.3447	530	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	82.0628	847	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_018069755.1	s__Ideonella sp018069755	81.9522	833	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710065.1	s__Ideonella sp016710065	81.3424	714	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	99.07	99.00	0.95	0.93	3	-
GCA_016213265.1	s__Ideonella sp016213265	81.1789	704	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010499455.1	s__Ideonella sp010499455	81.1387	746	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780145.1	s__Ideonella sp018780145	81.0447	736	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004016515.1	s__Rubrivivax albus	80.1781	697	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216565.1	s__Leptothrix mobilis	80.1614	641	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Leptothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003265685.1	s__Piscinibacter caeni	80.0596	712	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938815.1	s__Rubrivivax sp903938815	79.7081	608	1554	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	99.66	99.41	0.96	0.94	10	-
GCF_014197795.1	s__Rhodospira goensis	75.5659	206	1554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	75.1869	233	1554	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565155.1	s__T1Sed10-7 sp003565155	74.7642	91	1554	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:11:28,941] [INFO] GTDB search result was written to GCF_024055665.1_ASM2405566v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:28,941] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:28,944] [INFO] DFAST_QC result json was written to GCF_024055665.1_ASM2405566v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:28,945] [INFO] DFAST_QC completed!
[2024-01-25 19:11:28,945] [INFO] Total running time: 0h3m23s