[2024-01-24 15:10:36,387] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:36,389] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:36,389] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f798645-9e6e-4f27-841f-6ed6042ef21a/dqc_reference
[2024-01-24 15:10:40,103] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:40,105] [INFO] Task started: Prodigal
[2024-01-24 15:10:40,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg1dec34f3-400c-486d-9a4e-85ff02a46de7/GCF_012927045.1_ASM1292704v1_genomic.fna.gz | prodigal -d GCF_012927045.1_ASM1292704v1_genomic.fna/cds.fna -a GCF_012927045.1_ASM1292704v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:02,211] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:02,212] [INFO] Task started: HMMsearch
[2024-01-24 15:11:02,212] [INFO] Running command: hmmsearch --tblout GCF_012927045.1_ASM1292704v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f798645-9e6e-4f27-841f-6ed6042ef21a/dqc_reference/reference_markers.hmm GCF_012927045.1_ASM1292704v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:02,653] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:02,654] [INFO] Found 6/6 markers.
[2024-01-24 15:11:02,718] [INFO] Query marker FASTA was written to GCF_012927045.1_ASM1292704v1_genomic.fna/markers.fasta
[2024-01-24 15:11:02,719] [INFO] Task started: Blastn
[2024-01-24 15:11:02,719] [INFO] Running command: blastn -query GCF_012927045.1_ASM1292704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f798645-9e6e-4f27-841f-6ed6042ef21a/dqc_reference/reference_markers.fasta -out GCF_012927045.1_ASM1292704v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:03,895] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:03,898] [INFO] Selected 14 target genomes.
[2024-01-24 15:11:03,899] [INFO] Target genome list was writen to GCF_012927045.1_ASM1292704v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:03,906] [INFO] Task started: fastANI
[2024-01-24 15:11:03,906] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dec34f3-400c-486d-9a4e-85ff02a46de7/GCF_012927045.1_ASM1292704v1_genomic.fna.gz --refList GCF_012927045.1_ASM1292704v1_genomic.fna/target_genomes.txt --output GCF_012927045.1_ASM1292704v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:26,232] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:26,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f798645-9e6e-4f27-841f-6ed6042ef21a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:26,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f798645-9e6e-4f27-841f-6ed6042ef21a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:26,249] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:26,249] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:26,250] [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
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	100.0	2168	2171	95	conclusive
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	88.3918	1598	2171	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	87.5548	1541	2171	95	below_threshold
Azohydromonas lata	strain=NBRC 102462	GCA_001571085.1	45677	45677	type	True	86.7456	1478	2171	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	80.6443	745	2171	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	80.5671	856	2171	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	80.5103	753	2171	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000420125.1	316997	316997	type	True	80.4632	797	2171	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	80.3256	812	2171	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	80.2846	772	2171	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	80.0987	728	2171	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	79.6408	743	2171	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	79.4847	733	2171	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	79.1911	688	2171	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:26,255] [INFO] DFAST Taxonomy check result was written to GCF_012927045.1_ASM1292704v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:26,256] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:26,257] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:26,257] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f798645-9e6e-4f27-841f-6ed6042ef21a/dqc_reference/checkm_data
[2024-01-24 15:11:26,260] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:26,326] [INFO] Task started: CheckM
[2024-01-24 15:11:26,327] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012927045.1_ASM1292704v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012927045.1_ASM1292704v1_genomic.fna/checkm_input GCF_012927045.1_ASM1292704v1_genomic.fna/checkm_result
[2024-01-24 15:13:11,265] [INFO] Task succeeded: CheckM
[2024-01-24 15:13:11,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:13:11,285] [INFO] ===== Completeness check finished =====
[2024-01-24 15:13:11,285] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:13:11,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012927045.1_ASM1292704v1_genomic.fna/markers.fasta)
[2024-01-24 15:13:11,287] [INFO] Task started: Blastn
[2024-01-24 15:13:11,287] [INFO] Running command: blastn -query GCF_012927045.1_ASM1292704v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f798645-9e6e-4f27-841f-6ed6042ef21a/dqc_reference/reference_markers_gtdb.fasta -out GCF_012927045.1_ASM1292704v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:13:13,708] [INFO] Task succeeded: Blastn
[2024-01-24 15:13:13,713] [INFO] Selected 8 target genomes.
[2024-01-24 15:13:13,713] [INFO] Target genome list was writen to GCF_012927045.1_ASM1292704v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:13:13,719] [INFO] Task started: fastANI
[2024-01-24 15:13:13,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg1dec34f3-400c-486d-9a4e-85ff02a46de7/GCF_012927045.1_ASM1292704v1_genomic.fna.gz --refList GCF_012927045.1_ASM1292704v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012927045.1_ASM1292704v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:13:30,345] [INFO] Task succeeded: fastANI
[2024-01-24 15:13:30,353] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:13:30,354] [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_012927045.1	s__Azohydromonas caseinilytica	100.0	2168	2171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000430725.1	s__Azohydromonas australica	88.4153	1595	2171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760915.1	s__Azohydromonas aeria	87.6088	1534	2171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571085.1	s__Azohydromonas lata	86.7668	1475	2171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	81.0712	959	2171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003569765.1	s__Aquabacterium_B tepidiphilum	81.0436	946	2171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969605.1	s__Aquincola tertiaricarbonis	80.6904	1013	2171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	80.5567	889	2171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:13:30,356] [INFO] GTDB search result was written to GCF_012927045.1_ASM1292704v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:13:30,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:13:30,361] [INFO] DFAST_QC result json was written to GCF_012927045.1_ASM1292704v1_genomic.fna/dqc_result.json
[2024-01-24 15:13:30,362] [INFO] DFAST_QC completed!
[2024-01-24 15:13:30,362] [INFO] Total running time: 0h2m54s