[2024-01-24 12:13:27,551] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:27,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:27,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d7eef7e-b331-43ba-8955-4868245c5fd8/dqc_reference
[2024-01-24 12:13:28,991] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:28,992] [INFO] Task started: Prodigal
[2024-01-24 12:13:28,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg748729bc-2ec6-4ce2-8b5a-024423706cdf/GCF_003008515.1_ASM300851v1_genomic.fna.gz | prodigal -d GCF_003008515.1_ASM300851v1_genomic.fna/cds.fna -a GCF_003008515.1_ASM300851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:41,675] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:41,676] [INFO] Task started: HMMsearch
[2024-01-24 12:13:41,676] [INFO] Running command: hmmsearch --tblout GCF_003008515.1_ASM300851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d7eef7e-b331-43ba-8955-4868245c5fd8/dqc_reference/reference_markers.hmm GCF_003008515.1_ASM300851v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:42,034] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:42,035] [INFO] Found 6/6 markers.
[2024-01-24 12:13:42,075] [INFO] Query marker FASTA was written to GCF_003008515.1_ASM300851v1_genomic.fna/markers.fasta
[2024-01-24 12:13:42,075] [INFO] Task started: Blastn
[2024-01-24 12:13:42,075] [INFO] Running command: blastn -query GCF_003008515.1_ASM300851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d7eef7e-b331-43ba-8955-4868245c5fd8/dqc_reference/reference_markers.fasta -out GCF_003008515.1_ASM300851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:43,247] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:43,250] [INFO] Selected 21 target genomes.
[2024-01-24 12:13:43,251] [INFO] Target genome list was writen to GCF_003008515.1_ASM300851v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:43,259] [INFO] Task started: fastANI
[2024-01-24 12:13:43,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg748729bc-2ec6-4ce2-8b5a-024423706cdf/GCF_003008515.1_ASM300851v1_genomic.fna.gz --refList GCF_003008515.1_ASM300851v1_genomic.fna/target_genomes.txt --output GCF_003008515.1_ASM300851v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:06,860] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:06,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d7eef7e-b331-43ba-8955-4868245c5fd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:06,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d7eef7e-b331-43ba-8955-4868245c5fd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:06,882] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:06,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:06,883] [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
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	100.0	1497	1498	95	conclusive
Phreatobacter oligotrophus	strain=DSM 25521	GCA_003046185.1	1122261	1122261	type	True	86.4688	1147	1498	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	80.8761	981	1498	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	78.6751	588	1498	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	78.6631	628	1498	95	below_threshold
Chelatococcus composti	strain=DSM 101465	GCA_018398355.1	1743235	1743235	type	True	78.5629	432	1498	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	78.5	526	1498	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	78.3997	400	1498	95	below_threshold
Microvirga lenta	strain=SM9	GCA_020532555.1	2881337	2881337	type	True	78.3563	393	1498	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	78.075	458	1498	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	78.063	477	1498	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	77.8281	458	1498	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.7889	598	1498	95	below_threshold
Xanthobacter aminoxidans	strain=ATCC BAA-299	GCA_023571765.1	186280	186280	type	True	77.7768	498	1498	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	77.7645	503	1498	95	below_threshold
Bradyrhizobium nitroreducens	strain=TSA1	GCA_002776695.1	709803	709803	type	True	77.6868	510	1498	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.6858	632	1498	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	77.6706	535	1498	95	below_threshold
Microvirga pudoricolor	strain=BT291	GCA_016892705.1	2778729	2778729	type	True	77.6446	346	1498	95	below_threshold
Methylobacterium adhaesivum	strain=DSM 17169	GCA_022179065.1	333297	333297	type	True	77.5229	359	1498	95	below_threshold
Methylobacterium goesingense	strain=DSM 21331	GCA_022179225.1	243690	243690	type	True	77.4619	376	1498	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:06,884] [INFO] DFAST Taxonomy check result was written to GCF_003008515.1_ASM300851v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:06,885] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:06,885] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:06,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d7eef7e-b331-43ba-8955-4868245c5fd8/dqc_reference/checkm_data
[2024-01-24 12:14:06,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:06,933] [INFO] Task started: CheckM
[2024-01-24 12:14:06,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003008515.1_ASM300851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003008515.1_ASM300851v1_genomic.fna/checkm_input GCF_003008515.1_ASM300851v1_genomic.fna/checkm_result
[2024-01-24 12:15:14,748] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:14,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:14,774] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:14,775] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:14,775] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003008515.1_ASM300851v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:14,776] [INFO] Task started: Blastn
[2024-01-24 12:15:14,776] [INFO] Running command: blastn -query GCF_003008515.1_ASM300851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d7eef7e-b331-43ba-8955-4868245c5fd8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003008515.1_ASM300851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:17,080] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:17,084] [INFO] Selected 8 target genomes.
[2024-01-24 12:15:17,084] [INFO] Target genome list was writen to GCF_003008515.1_ASM300851v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:17,090] [INFO] Task started: fastANI
[2024-01-24 12:15:17,090] [INFO] Running command: fastANI --query /var/lib/cwl/stg748729bc-2ec6-4ce2-8b5a-024423706cdf/GCF_003008515.1_ASM300851v1_genomic.fna.gz --refList GCF_003008515.1_ASM300851v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003008515.1_ASM300851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:28,762] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:28,775] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:28,775] [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_003008515.1	s__Phreatobacter cathodiphilus	100.0	1498	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001464235.1	s__Phreatobacter sp001464235	91.2211	1087	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046185.1	s__Phreatobacter oligotrophus	86.474	1147	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793595.1	s__Phreatobacter sp016793595	83.7894	1057	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005160265.1	s__Phreatobacter sp005160265	81.736	978	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000751295.2	s__Phreatobacter sp000751295	81.5974	996	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304475.1	s__Phreatobacter sp017304475	81.3664	1004	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144885.1	s__Phreatobacter stygius	80.8411	986	1498	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:28,779] [INFO] GTDB search result was written to GCF_003008515.1_ASM300851v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:28,781] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:28,788] [INFO] DFAST_QC result json was written to GCF_003008515.1_ASM300851v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:28,789] [INFO] DFAST_QC completed!
[2024-01-24 12:15:28,789] [INFO] Total running time: 0h2m1s